The original issue was fixed and released in Scala 3.3.2 / 3.3.3 - see coverage changelog for Scala 3.3.3 Release 3.3.3 · scala/scala3 · GitHub
It contains both fixes mentioned in the original issue: Compiler produces incorrect/incomplete coverage data · Issue #16634 · scala/scala3 · GitHub
I guess your problems might be related to some other issues. In such a case, we’d require a reproducer to fix it.
If you’ve used exclusions for coverage reports in Scala 2, then these were added in Scala 3.3.4 (as a backport from 3.4.2)(Port coverage filter options for packages and files by KacperFKorban · Pull Request #19727 · scala/scala3 · GitHub)